Though the Heavens Fall
by SheepyTheSheep
Summary: Gendo Ikari has found a use for his son earlier in his life. How will this Shinji fare in the machinations of SEELE and NERV? An AU where Shinji is not a wuss while still being a push-over. Rated M for some scenes (mainly medical in nature). (Cover is from the Rebuild page on Wikipedia)
1. Chapter 1

**Author Note:** I kinda butchered some of the early timeline but I had to make some of the stuff work for the fic. Please forgive me.

 **Disclaimer:** I do not own Evangelion or anything related to it. I only write stuff.

* * *

 **NERV Priority Transmission Log 0925629H-98**

 **Encryption Code:** X-Ray

 **Public Key:** Cole/execBeta/

 **From:** Dr. Ritsuko Akagi M.D., Ph.D., Head of the NERV Tokyo-3 Science Department, NERV Japan

 **To:** Commander Gendo Ikari, Commander-in-Chief of NERV, aboard the NERV Shuttle _Endeavor_ exiting NERV Luna Base

 **Subject:** Unit-01 Activation Test Results and Analysis

 **Classification:** Restricted (Eyes Only)

/start transmission/

Commander,

As per your orders, the Science Division and I have started looking into the data relating to the Third Child and the recent Unit-01 Activation Test. The results are as follows (although I do advise further synch tests to gauge the pilot's innate ability to synch with the EVA):

 **Initial Synch Ratio:** Bordering between an initial 40~43% at first synch.

The Initial Synch Ratio was surprising given that the subject has not even reached puberty. Further tests including exclusion of the plugsuit is recommended. Pushing the borderline up should work since the mental contamination during initial synch was an inconsequential value.

 **Conclusion** : The Third Child is to be submitted to further testing.

 **Psych Evaluation:** Subject was denied a psych evaluation as per the NERV Commander's orders.

I do hope you know what you're doing to the subject.

 **Conclusion** : No available data.

 **Physical Evaluation:** Subject has been cleared with a clean bill of health.

Despite being healthy enough, I have already advised the facility trainers to begin the Third Child for intense combat training; this is to ensure a bleed-effect1 into EVA piloting.

 **Conclusion:** Subject unfit for active duty; direct intervention necessary.

The other data gathered is attached to the message. I hope to again study the Third Child in a month's time; this time on-site if possible.

 **Attachment:** Encryption /E

/end transmission/

Press **ENTER** to open linked attachments.

* * *

 **06-06-2009**

"Good evening Third Child. It seems you are taking the augmentations rather well."

The young boy, no more than 8 years old, could not answer back. For presently, he was strapped down on a gurney with a gag over his mouth. A series of tubes ran down along his arms. The tubes were connected to a machine that was pumping a series of chemicals into his bloodstream. The strain of the operation was evident by the mask of pain that adorned his face.

"I heard it was your birthday today, Third Child. As per orders, your gift from the commander is an augmented eye."

The man's feral grin only served to drive the boy into hysteria as a robotic surgical arm descended from the upper levels of the operation room. The arm extended; flexing its joints as it moved with surgical precision. A needle as large as a finger was attached to appendage by a short, stocky medical assistant. Before he could protest, the boy's head was abruptly snapped back down as a pair of hands secured his forehead and jaw to the gurney using straps. He was facing towards the ceiling as two thin hooks were used to keep his left eye open. The pain of the piercing was nothing compared to the horror that followed. The now needle-equipped arm was summarily positioned above the center of his eye. Before it could descend, he tried to wiggle his head left and right but to no avail. The straps were too tight. He tried moving the eye about but the advanced paralytic agent rendered him unable to move consciously. Soon the agent was in full effect. Locomotion was denied to him but the pain still remained. The Professor had always told him that pain was meant to be felt to measure a man's worth. Right now, he imagined he was worth millions. The needle descended and began to bore into the eye. The boy could only shout in his mind as waves of pain began racking his frame and his body took the punishment lying down as if the pain were non-existent. Before he passed out, he heard the Professor mutter.

"Happy Birthday, Shinji."

* * *

 **08-16-2009**

"Alright Third Child, today we are activating EVA Unit-01. It is a Test-Type model; regardless the Commander has deemed it fit to see the procedures first hand. Do you have any questions?"

The boy merely shrugged and began donning his neural interface plugsuit. The A-10 clips, while not yet perfected, were also put on. The plugsuit was an unremarkable gray; testament to NERV Luna Base's military background. A pair of handlers flanked him as he was escorted to the entry plug loading bay. A pair of blast doors hissed open and he was greeted by the sight of a hundred technicians floating about. Unit-01's entry plug was situated in the middle of all the chaos. Casually pushing off the ground, the Third Child propelled himself to the open hatch. A solitary technician was waiting to seal him in. With a slight nod to the waiting tech, the Third Child slipped inside the entry plug and began situating himself on the familiar seat. The hatch was closed and sealed as a speaker icon flashed to life in the main screen; the words 'audio only' were plastered in bright orange text. Gripping the entry plug control yokes, the Third Child waited as the system technicians began counting down the final stages of preparation.

"Stage Three cooling process complete! Beginning power siphon of EVA Unit-01."

"Terminal signal plug ejecting!"

"Ejection confirmed. Unit-01 entry plug inserting in 3, 2, 1. Insertion complete."

"Releasing spinal cord transmission system and establishing connection to the plug."

"Connection established! Mental contamination within acceptable parameters."

"Begin flooding the plug with LCL."

A series of hatches opened from within the entry plug. The orange LCL fluid began streaming in. The Third Child closed his eyes and breathed in deeply once the LCL passed head level.

"Entry plug flooded. LCL level stable. Pilot bio-signs are normal and holding."

"Establishing neural handshake. Pilot, commence synch."

A sudden wave of nausea assaulted him. However, the brief discomfort soon passed and he could feel himself floating; as if becoming one with the EVA.

"Initial synch ratio at 40% and holding. No sign of mental contamination."

"Copy that bridge crew. Secondary umbilical detaching."

"Primary umbilical is supplying steady power."

"Command, we have activation!"

Before he knew it, a series of cheers rang out from the Luna Base tech crews. He sighed in relief as he basked in the warmth offered by the EVA. It felt nice inside the behemoth. He couldn't place it but it felt as if he were protected within its embrace. Shaking off his wayward thoughts, he immediately clicked the communications transmission button for the bridge.

"Professor, what is my next objective?"

"Third Child, you are to hold or surpass the 40% synch ration for now. Congratulations, you are fit to be a pilot."

The boy broke into a grin. It would seem that he was good at something.

* * *

 **01-11-2010**

Shinji stood at ease. Being the Third Child meant a certain amount of decorum was demanded of him. As such, the boy stood stock still as he was lectured by the Professor regarding the day's training run.

"Third Child, today we test your ability to react to unknowns in a combat situation." A screen flashed to life behind the professor that showed the overlook of Aitken basin, the largest visible crater on the moon. "In the middle of the basin is an abandoned NERV landing craft. Your mission is to neutralize the craft."

Shinji didn't need to ask what was in store for him. He knew that the whole setup was trouble. Fixing his gaze forward he nodded once.

"You will be deployed in Unit-01 at the southwestern edge of the basin. You will be given 5 minutes of power to cover the distance and neutralize the craft. Any questions?"

Shinji merely shook his head once and was then summarily dismissed. He clutched his A-10 clips in one hand, and a folded up plugsuit in the other. Marching along, he arrived at the changing rooms to ready himself for the combat exercise. Donning his clips and suit, the Third Child took steady breathes before making his way to the entry plug chamber. The wail of warning sirens signaled his imminent deployment onto the moon's surface. Clambering aboard the plug, he seated himself and began the preliminary system checks drilled into him since the activation test. A communications window winked to life and he was greeted by the face of the Professor.

"Third Child, all systems are nominal. Ready yourself for the LCL flooding."

Without warning, the hatches opened and the plug was flooded. The orange fluid smelled like blood but he was not one to complain. In fact, the scent was comforting – in a way. Breathing in deeply, he began counting down the seconds till they began the neural handshake. The wave of nausea was the indication, followed by the warmth of the EVA powering up. He breathed and the EVA breathed with him. It felt amazing to be able to control the huge construct.

"Unit-01 is ready for launch deck crew. Relocate EVA to launch bay 09-A. Designation Aitken Gate."

"Copy that bridge. Unit-01 in transit."

Shinji felt the rumble of the EVA cage as the tracks rotated to send him to the launch bay. Closing his eyes, he established the neural link to Unit-01. Upon opening his eyes, he was greeted with a view of the launch corridor. Keying in the communications to the bridge, he began his launch procedure.

"Ikari, Shinji on Unit-01. Neural handshake accepted. Synch is green. Ready for ascent."

"Copy that Third Child. Brace yourself."

That was the only warning he got before he was launched up at frightening speeds. He briefly entertained the idea of breaking the restraints and doing a somersault when he exited the Aitken Gate. With a slight grin, he banished the thoughts in favor of focusing on the mission. Readjusting his grip on the control yokes, the Third Child braced himself as the g-forces threatened to knock him out. Concentrating and doing the appropriate blood regulation exercises taught to pilots, he was able to stay conscious for most of the trip.

After what seemed like an eternity, a series of blast doors greeted him signaling his arrival at Aitken basin's gate. The twin titanium grade doors ground open and the EVA cage slammed to a halt on the surface. Regaining his senses, he listened as the technicians began the final release of Unit-01.

"Decoupling external locks. Primary umbilical cable is detaching. Pilot, you have exactly 5 minutes and 45 seconds of power left. God speed."

Not wasting any more time. Shinji brought the EVA into a run as soon as the cage locks released him. Usually, he would scope out the battlefield first for potential threats before proceeding. This time, however, he was not afforded that luxury. 5 minutes meant that he would have to think on his feet; exactly what the exercise demanded of him. Ahead of him the basin stretched out. Nearing the basin's lip, he brought up the EVA's structural integrity report. It looked like Unit-01 had undergone a complete refit after the last exercise. Smiling at the memory, Shinji began calculating his jump trajectory. Gravity still played a factor given the sheer mass of his EVA. Bracing himself for the drop, Shinji leapt. The EVA formed an arc, landing 500 meters from the lip. The basin was 2500 kilometers across. Science told him it was impossible to cover that distance in 5 minutes. The EVA, however, egged him on. The Professor had stated that the NERV craft was at the center. Common sense told him it was impossible for the craft to be dead center due to the fact that he could never reach it in time. Smiling, he began using his external relays to scan for anything resembling a pre-impact Gehirn craft. Gehirn in the old days would have used one of the shuttles to get preliminary data on the moon. It meant that the NERV shuttle was in fact one of the Gehirn landers. 3 pings came back positive and he triangulated each position of the pings by piggybacking on the signals of the satellites orbiting Earth. What surprised him, however, was the threat alert he received when he tried to proceed further into the crater. Glancing at his energy clock, he saw that he only had 4:52:21 left. Double timing his pace, he faced the direction where the threat detection system identified a potential threat. At first there was nothing in front of him, then suddenly the basin floor began shaking and a rock face to his front began sliding open. Before he could assess the situation, a trio of missiles streaked out and headed for his EVA. Thinking on his feet, he had the EVA roll to the side so the missiles could streak past him. Bringing up the weapon systems, he realized he only had the standard issue Progressive Knife equipped. Cursing his forgetfulness, he decided that he needed to close the distance in the event that his enemy had even more ranged weaponry. Inching forward at a jog he came face to face with an almost humanoid robot as big as his EVA. Bringing up his HUD threat indicator, the Friend-or-Foe system brought up the robot's identification. It was classed as the Jet Alone Mk.1. No further information was given. Glancing at the Jet Alone Mk.1, one would not take it for a weapon of mass destruction. Its next actions stated otherwise.

The Mk.1 faced his EVA and began a power-up cycle. A whine could have been heard had they not been in zero gee. The only indication was the slight shaking of the frame as the machine began advancing towards him at a frightening pace. His system diagnostics began going haywire as a spike in the Geiger counter showed. It looked like the Mk.1 was about to detonate its nuclear core. Shinji knew that he didn't have time to escape the blast radius. Discarding the prog-knife, the EVA began extending its arms forward, palms out. Back in Luna Base, technicians were getting somewhat unbelievable readings on the pilot's bio-monitors.

"Sir, pilot heart rate has sped up. Synch ratio increasing from 60% and climbing steadily!"

"EVA is generating an A.T. Field sir!"

"Pilot synch ratio at 89% percent and holding. Mk.1 is set to detonate sir!"

Worried glances were exchanged as the Professor, head of Luna Base, contemplated whether the Mk.1 needed to be detonated. It was supposed to be a threat that the pilot had to accept. The exercise was supposed to teach the Third Child that not all situations were always going to end in their favor; it was a lesson meant to teach how it felt like to lose a battle. The A.T. Field generation threw a wrench in their plans. The Third Child was still not supposed to be able to do that. It would seem that they needed to closely monitor the EVA training sessions he had from now on. Sighing, the Professor keyed in the detonation code.

"Sir! Mk.1 is live! Detonation in t-minus 8 seconds."

Up above, Shinji braced himself as one of the world's deadliest weapons predating the N2 mine readied to detonate a mere 2 kilometers from his position. Pouring all his concentration into keeping the A.T. Field up, Shinji watched as the Mk.1 went up in a mushroom cloud of devastation. The shockwave reached him before he was engulfed in fire. As quickly as the flames appeared they were gone. Extinguished by the lack of air. By some miracle, his A.T. Field held. He had been thrown back a few kilometers by the shockwave but the damage to the EVA was negligible. Laughing, he began pinging for the Gehirn craft. Before he could proceed further the Professor's face cam winked to life on his HUD.

"Good work pilot. Today's training exercise has been postponed. Power down and await retrieval."

Puzzled, Shinji could only comply and wait for extraction. He wondered what he did wrong.

* * *

 **10-12-2013**

At 12 years of age, Shinji Ikari was easily the best EVA pilot NERV had to offer. Only the Commander, the head of the Science Department, and the NERV Luna Base knew of his existence. It was all about to change soon. Gendo knew that the 3rd Angel was due to appear at any given time. It was then that he would play his card and reveal the existence of the Third Child. SEELE, of course, knew of his existence. However, they did not know where he was situated. Most speculated that he was housed in NERV Tokyo-3. Gendo merely let them assume. They would know soon enough. Glancing at the two-way mirror, the Commander watched as Dr. Akagi continued to evaluate the Third Child's psyche. He himself knew of his son's problems, however it would not do for the scenario to be jeopardized by a misplaced sense of compassion from him. Yui knew what the EVA project entailed and she sacrificed herself for its advancement. Shinji was merely a means to an end. He would be with Yui and Shinji would only be a stepping stone. After all, what was a son without the mother? Can he really be considered his if the person that birthed him was no longer alive? Shinji, to him, was a minor inconvenience. Instrumentality would be his so mold, let the world burn for all he cared. Reorganizing his stoic mask, he returned his gaze to the room and found that Shinji was finally done with the psyche evaluation and the Doctor had excused herself from the room to join him. The hissing of the door opening was the only indication that Dr. Akagi had moved to join him in observation.

"He seems to be well adjusted for someone that underwent the augmentation procedures I've read about."

"He is a post-impact Child. He must be resilient to weather the coming storm."

With that, Gendo Ikari strode out of the room, the doctor in tow. It looked like NERV was finally ready.

* * *

 **Early 2015, A few hours before the appearance of the 3** **rd** **Angel**

"All hands to stations. Prep EVA Unit-01 for atmospheric re-entry."

Klaxons blared to warn off all personnel not equipped with zero gee suits in the Luna Base hangar. People in bright orange space suits flitted about in preparation for the departure of the Third Child. Shinji could only watch as his entry plug was readied to be inserted into Unit-01. The entry plug was placed inside a tube that fed into the room where he was to enter. While amusing that they only tried this procedure now, Shinji knew that the real problem lay in his re-entry vessel. Taking a glance at the situation, he could see that technicians were still inspecting the structural integrity of the landing craft. He was told yesterday that they were still unsure as to whether the craft would hold during atmospheric re-entry. Sighing to himself, he began preparing instead of worrying about a scenario where he gets fried during re-entry. Much to his chagrin, he noticed that his plugsuit had been refitted as a thermal suit along with a neural helmet. The technicians, with the input of Dr. Akagi, had stated that the LCL could come to a boil given that the EVA could be thrown free of the re-entry shuttle. As such, he needed to be tempered for the heat if his EVA were to free fall from the atmosphere. Donning that rather bulky suit and tucking his helmet under one arm, Shinji exited the locker rooms and was greeted by the Professor.

"Third Child, walk with me."

Gesturing with his hand to follow, the Professor began walking along the view deck of Hangar 08; the hangar that housed EVA Unit-01. Quickly catching up and matching the Professor's step, Shinji walked beside the man who taught him everything he knew.

"Third Child, I know that the first few years of training have been rough for you. Rest assured, the augmentations made to your body will not fail you in your time of need."

Shinji knew when a person was uncomfortable discussing something. He knew that the Professor was skirting from the actual conversation he wanted with Shinji.

"Professor, I know everything by heart. Do you doubt my capabilities?"

"Your father would. I however, am not him, despite being related by blood. You may call me Uncle from now on Shinji. I know it is what Yui would have wanted."

His uncle did not turn around when the Section 2 agent announced that the entry plug had been prepped and they were all waiting on him. Shinji could not understand where the sentimentality was coming from. In all his years under the Professor's tutelage, he was never addressed as anything but the Third Child; a means to an end. Why now of all times to show a hint of compassion? Deciding that the answer was not worth the trouble, he bade his uncle farewell and departed with the Section Two agent. The last glimpse Shinji had of his uncle was with his back to him. Staring blankly at the locked Unit-01.

The elevator dinged and Shinji was swept into Hangar 08. The Section Two agent was walking beside him and he was instructed to follow the technician leading them. They arrived at a circular room with artificial gravity. The entry plug was situated in the center of the room inside a tube that shot directly into the terminal plug of the EVA.

"Good morning pilot. I trust that you have been briefed on the procedure?"

"Yes sir. The Professor had me run preliminary simulations prior to the drop date."

"Good, good. If you don't mind, please enter the entry plug so that we may begin."

Donning his neural helmet, he climbed aboard the plug and sealed himself in. The magnetic locks clicked and he was shrouded in darkness. After a few moments, a faint beep was heard and the entry plug powered up. Lights began flickering on and his HUD sprang to life.

"Entry plug receiving preliminary power. Pilot suit powered up. Drop commence."

The entry plug sprang into motion as it was shot down the tube connecting to the EVA's terminal plug. Shinji's stomach lurched as gravity set in. After a few moments, the entry plug ground to a halt and the familiar 'audio only' text flickered to life on his HUD.

"Structural integrity of entry vessel at 100%. EVA is set to synch with pilot."

"Copy that deck crew. Flooding entry plug with LCL."

"Entry plug flooded. Commence neural handshake."

"Handshake accepted. Mental contamination within acceptable levels."

"Pilot, walk the EVA into the re-entry vessel cage."

"Copy that tower. EVA in motion."

Shinji focused on walking and the EVA walked with him. He strode forward and proceeded to step into the EVA cage within the pod like craft. Powering down the system, he waited for the locking mechanisms to secure him to his ride.

"Primary and secondary locks holding. External power source and umbilical cable set. EVA functioning at 80% capacity. Power usage optimal for 5 hours of continuous use as long as the umbilical is attached."

"Copy that tower. Bridge crew sealing re-entry vessel."

A thunderous clap was heard as the 5-meter thick, titanium blast doors sealed his EVA inside the pod. He breathed in and out as the video feed showed him nothing but darkness.

"Third Child, switch to external cameras to monitor your descent vector. Switch to auto pilot when you enter the Earth's atmosphere."

"Copy that tower, will do."

"Shinji, NERV Tokyo-3 relayed a message. It seems like the blue pattern of an Angel was detected already a few kilometers off the shore of Tokyo-3. You may be deployed into a raging battle so be careful out there."

Wincing at the show of concern, Shinji decided that proceeding as normal would be his best option.

"Copy that Professor. Third Child, out."

With a look of slight disappointment, the Professor killed his video feed. His voice, however, could still be heard in the Luna Base announcement system.

"Attention all personnel. Silence on the comms. Countdown till EVA drop is 10 minutes. I repeat, countdown till EVA drop is 10 minutes. Prepare the pod for re-entry. All non-essential personnel please clear the bridge. Control tower, you have operation control."

"This is tower to Unit-01. You are clear for launch in t-minus 10 minutes."

A huge countdown timer appeared on his HUD. The number ticked down from 09:54:12 while he ran a secondary system diagnostic. The base bridge was unusually quiet for an operation this big. He hoped that he didn't blow his opportunity to prove his worth.

"Tower to Unit-01. You are clear for launch in t-minus 10 seconds. 9, 8, 7, 6, 5, 4, 3, 2, 1. Launch!"

Shinji braced himself as the twin engines sprung to life and blasted the hangar launch pad. Slowly the craft ascended while blast doors opened in rapid succession during his ascent. A few seconds later and he was rocketing away from Luna Base; a trail of exhaust the only indication he ever left.

"Re-entry vessel is away. Good luck Third Child."

"Copy that tower. Third Child out."


	2. Chapter 2

**Author Note:** Let me stress that this is an AU. Kozo, Rei, and the Commander have different views in this rendition of Evangelion. I want that to be clear in case questions come up. I also skipped Sachiel devastating the JSSDF because I really can't imagine how I'm supposed to write how VTOLs get rekt. On the topic of AUs, the next chapter will be more of a background as to why Kozo and Rei act this way (in this chapter) and what had happened during Unit-00's Activation Test. Most likely I'll be uploading 2 chapters next time. One for the background and one for the 3rd Angel Battle. Enjoy.

 **Disclaimer:** I do not own Evangelion or anything related to it. I only write stuff.

* * *

 **JSSDF Service Record 09510-3H6**

 **Encryption Code:** Epsilon

 **Public Code:** /sigma/

 **Subject:** Lieutenant General Hideo Iwakuro

 **Date of Birth:** Born March 19, 1962 at 04:53:21 AM Pacific Standard Time

 **Place of Birth:** Kurahashi, Hiroshima Prefecture. (Now merged to Kure, Hiroshima)

 **Age of Retirement:** 53

 **Status:** MIA, possibly deceased

 **Career:** Lieutenant General Iwakuro entered the Nagoya Military Academy at the age of 18. Graduating with honors as 5th in his class of 40, the then lieutenant was assigned as platoon leader of the first squad of the 16th Infantry Regiment. Prior to 2nd Impact, majority of the JSSDF troop movement was relegated to internal security. The lieutenant managed to ascend the ranks through senior commendations, attaining the rank of captain. Later granted command of the 4th Armored, the captain led his troops during the post-Impact crisis. Eventually, his actions during the rescue and relief efforts afforded him a fast track to a major general position. At the age of 50, Iwakuro was promoted to Lieutenant General and given command of the JSSDF forces operating in the Kanto and Chubu regions of Japan. On the 6th of June, 2015, Lieutenant General Iwakuro was made operation commander of Operation First Contact. Details include the battle of Tokyo-3 where an Angel, codenamed Sachiel, had appeared. Further details of the operation are attached with X-ray level encryption (see end of record). After Operation First Contact, Lieutenant General Hideo Iwakuro submitted his resignation and his current whereabouts are unknown. It is believed that the General had posed as a security threat to the Global Security Organization of NERV and was summarily executed.

Press **ENTER** to decrypt and view Operation First Contact files.

* * *

 **06-06-2015 / Somewhere in high Earth orbit**

Breathe in, breathe out. The almost inaudible sound of an inhale and exhale could be heard as the Third Child, Shinji Ikari, ran the system diagnostics for what seemed like the hundredth time. Military standard time showed him that it was now 1200 hours, and that meant that he had been in stasis for close to 4 hours. Shinji knew better than to complain, but no one told him that Operation First Contact would take so long. The Commander had sent him text-only messages comprised of situation reports while he was in orbit. It looked like the Battle of Tokyo-3 was underway and that the JSSDF had taken control of the Operation. In his mind, the Third Child was frustrated beyond belief. They were wasting time. He knew based on research that conventional weaponry would do nothing to the Angel **.** A.T. Field generation alone would have rendered most weapons useless against an EVA, much less an Angel that inherently possessed an A.T. Field of its own. Taking a glance at his overall system's scan, Shinji decided on powering the EVA up to 100% capacity in case he was needed immediately. A ping distracted him from his musings. It looked like he'd received a message from NERV Tokyo-3. Quickly blinking to acknowledge the notification, the message opened up.

 _Come._

Poetic, he thought. It was just like the Commander to get right to the gist of the message. Grinning in anticipation, he began cycling the re-entry vessel's generator; performing the necessary checks to ensure that the craft would survive re-entry. A soft rumble indicated that the craft was on the move. Switching to external cameras, he was greeted by a view of the stars and the Earth. Marveling at the spectacle, Shinji committed the sight to memory. The moment soon passed and with it his amusement. He had to focus on the mission. Once the vessel reached the right altitude, the auto-pilot was switched on to facilitate his descent. Attaching the restraints to his suit, the Third Child braced himself for what would promise to be a bumpy ride down.

* * *

 **06-06-2015 / NERV HQ, Tokyo-3**

"My god, the thing's still alive!"

"That was an N2 mine! This is impossible!"

"Evacuate the Geo Front immediately! We need to regroup and reassess back at Tokyo-2!"

"ENOUGH!"

Silence immediately descended within the NERV HQ command room. The speaker, Lieutenant General Iwakuro of the JSSDF, looked at all the men under his command then stared at the NERV Commander without flinching.

"It is to my shame that I acknowledge that the JSSDF was combat ineffective in Operation First Contact. Thus said I will shoulder the blame for the failure of the operation and I hereby relinquish operation control to NERV and its commander."

With that, the Lieutenant General bowed deeply and exited the room with an about-face, along with his aides. The rest of the JSSDF command followed suit after what seemed like minutes; recovering from the shock of their leader leaving.

Meanwhile, Gendo Ikari reveled in his new-found power. Of course he had known that the scenario would play out like so. It was just icing on the cake to know that the now shamed Lieutenant General would be a target for SEELE since he had seen too much into the Operation. Clasping his gloved hands together, the Supreme Commander of NERV gestured for Vice Commander Fuyutsuki to take command of the situation. With a puzzled glance, his right hand man decided to ask the question on everyone's mind.

"Gendo, how do we fight the Angel without a functional EVA and pilot?"

Smiling, the bespectacled man sent the message to the waiting Unit-01 orbiting Earth. Satisfied that his summons had been received he faced his Vice Commander.

"Have Rei take Unit-00 out to sortie."

"Sir, the First Child is in no condition to pilot. Despite the successful activation of the EVA, the injuries incurred are still too grievous for her to pilot effectively."

"Vice Commander, I understand your attachment to the First Child. However, I will not allow a misplaced sense of paternal instinct jeopardize the fate of the world. Have EVA Unit-00 ready to sortie. Major Katsuragi, you will be Operations Director while I attend to other matters."

With that the Commander of NERV stood and exited the command room. Regaining his composure, Kozo Fuyutsuki cursed the day he was coerced to work with one Gendo Ikari.

"Major Katsuragi, I will attend to the First Child. Please have Unit-00 prepared for combat."

Striding across the room, Kozo entered the departmental lift and keyed in the floor for the secure medical wing. He left the crew to handle the logistics of preparing an EVA for combat. He was needed elsewhere. A brief trip down led him to a room marked 10-A. Sighing in resignation he pushed the door open. The sight that greeted him was that of a blue haired girl, no older than 14, reading a book whilst swathed in bandages. His entrance interrupted her activities and the girl looked up to address her visitor.

"Vice Commander, how are you today?"

"I am well Rei. Although I can say otherwise for you."

Smiling, Rei Ayanami put down her book and gave her full attention to the Vice Commander.

"I understand that you've been weaned off of the suppressants. However, I advise you to tone down your attitude change to remain under the Commander's radar."

"I understand. I will endeavor to suppress these new emotions to the best of my ability."

Offering Rei a small smile, the Vice Commander began to address the elephant in the room.

"Rei, it would seem that despite your injuries, the Commander would have you sortie with the Angel in Unit-00."

"It is of no consequence Vice Commander. After all, I am built to be replaced."

Clutching the girl's uninjured hand in frustration, Kozo decided that enough was enough.

"You are not replaceable. Do not ever consider yourself a throwaway human!"

"I understand Vice Commander. However, it is my duty to pilot."

With that final statement, Kozo Fuyutsuki could only watch as Rei Ayanami, designated First Child, prepared herself to die.

* * *

 **06-06-2015 / Inside Unit-00's entry plug**

"How are you doing Rei? Think you can stop that thing?"

"I do not know Major Katsuragi. We will have to see how the battle pans out."

"Look out for yourself. I still owe you that lunch you hear?"

With that, the display winked out and Rei was plunged into darkness.

"Flooding entry plug with LCL!"

Hatches overhead began opening and the small chamber was soon filled to the brim. Breathing in and out steadily, the First Child attempted to manipulate the EVA's control yokes. A lance of pain shot through her injured arm and she gasped in pain. Clutching at the throbbing appendage, the First Child was hit with an emotion she had not yet felt; despair. She did not want to die. The Major had promised her a lunch out if she managed to activate Unit-00. The Vice Commander had even suggested that as soon as she had recovered then they would be able to explore all of Tokyo-3 together; like a family. Back in the medical wing, she still had her emotions under control. Now, with the absence of the suppressants, coupled with the building pain from her injuries, Rei found that she could no longer control her reactions as easily. Sobbing in frustration at the pain and unfairness of it all, Rei decided that she still had much to live for. She would pilot or die trying. Clutching the control yokes tightly, the blue haired girl began her EVA synch cycle. Managing to keep her voice level, she managed to choke out her launch callouts.

"Ayanami, Rei in Unit-00. Neural handshake accepted. Synch is green. Ready for ascent."

"Copy that First Child. Unit-00 en route to Gate 12."

Rei could not answer back because the pain was unbearable. To pilot and synch to full effectiveness, the medical staff had purged all the anesthetics from her system. The heightened pain would help her focus on her own being therefore avoiding mental contamination from the EVA. Frankly, she could care less. She needed those painkillers. Whimpering in pain when her communication cut out, Rei strapped herself in as best as she could. The ride up would be harrowing but she needed to persevere.

"Unit-00 loaded into launch catapult. All systems are green. Proceed with launch."

A series of magnetic coils that served to propel the cage to the surface powered up and soon Rei found herself hurtling upwards. The pain felt even worse now. The g-forces pressing down on her, aggravated her already beaten body. Pressing her uninjured hand to her abdomen, Rei managed to avoid regurgitating the day's lunch. Before she could recover, the catapult ground to a halt and she found herself exiting the EVA cage. It was all so sudden. She needed a moment to reorient herself. Fate, however, had other plans for the First Child. All at once the sensors detected a blue pattern approaching Tokyo-3 from the east. The Angel itself stood high and mighty. Its hideous visage visible from where she was deployed. The Angel had stopped near the outskirts of Tokyo-3; silently assessing the new arrival.

When she focused on the Angel, her thoughts suddenly cleared and she was assaulted with images she could not place in her head. It seemed like the EVA had finally deemed her fit enough to synch with. An almost primal calm settled in her mind as the EVA regarded the Angel. She gripped the control yokes tightly despite the pain as Unit-00 drew its Pallet Rifle. Before she could even squeeze off a round, her HUD flashed a threat warning and suddenly the Angel was almost upon her. It had jumped forward using something like an A.T. Field to lift itself up. Propelling Unit-00 backward, Rei fired wildly. The rifle erupted with a staccato report of heavy armor piercing rounds. The Angel stomached the brunt of the burst without flinching. Without warning, Sachiel extended its arm and its energy lance manifested. Rei tried her hardest to shift the balance of EVA to dodge the stab but it was then that her injured arm gave way. The lance managed to puncture her EVA's eye and Rei felt her head erupt in pain.

"Sir! Angel just punctured all armor layers including the ablative coating! Pilot is entering into shock!"

"Rei listen to me! It's all in your head! You have to keep piloting! Someone get the entry plug life support online!"

"We can't Major. The EVA is rejecting commands from the command center."

"Hold on Rei! We'll get you out of there!"

The voice of Major Katsuragi filled her entry plug but Rei could no longer form coherent thoughts to answer. All she knew was pain. The Angel had her at its mercy and she could no longer do anything but accept death.

"Eject the plug!"

"EVA is blocking transmission signals ma'am. It won't respond!"

Rei watched as the Angel kicked out and sent Unit-00 flying back unto a building complex. The pain she felt rendered her helpless as the Angel advanced for the killing blow. Keying in her self-destruct sequence into the EVA mainframe, she could only hope to take the Angel along with her.

"The pilot has initiated the self-destruct system. Detonation in t-minus 1 minute!"

"Rei abort! You have to try ejecting the entry plug!"

"Negative, Major Katsuragi. My purpose is to pilot, and I will pilot till my last breath."

"Major! Pilot is disabling backdoor protocols! It's truly out of our hands now."

With grave looks, the NERV staff could only stare at the main screen as Unit-00's visuals displayed a countdown timer next to the approaching Angel. No one felt more helpless than Kozo. This was finally it. A scenario in which Rei would become reset. For the Commander, it would be another day at the office. For Kozo Fuyutsuki, it would be akin to losing family. His hands had the view deck railing in a vice grip. Any more and he would have bruised his fingers. When the countdown ticked down to less than 30 seconds the crew prepared themselves for the inevitable. Hunkered down within the EVA's entry plug, the First Child clutched her sides tightly as if to ward off death. Biting back the tears and the pain, Rei turned to face the Angel. However, before the countdown could reach below 15 seconds, a new voice interrupted the NERV comms.

"Unit-00, disable self-destruct. I repeat, disable the self-destruct system First Child. The Commander orders it."

Quickly terminating the countdown, Rei scrambled up to get a better view of whatever was coming. The EVA's sensors had detected a massive buildup of energy nearing Tokyo-3. She had assumed that it was the blue pattern at fault. What greeted her, however, was a sight so unlikely she wanted to try jumping for joy. The Vice Commander had stated that it was the appropriate response to exuberance and she knew she had exuberance in droves right now. What at first looked like a meteor was in fact a landing vessel akin to a drop pod. The NERV logo was etched on side in faded white paint. The vessel itself was shaped almost like a stocky teardrop and it was apparently in flames due to what she would assume was atmospheric re-entry. Tucking her injured arm to her side, Rei began keying in transmission codes to contact the unidentified ship. She needn't have worried about the Angel as well for Sachiel was also observing the object streaking towards them. Finally managing to hail the vessel's frequency, Rei opened a video feed to the NERV ship. A window appeared and she saw what appeared to be a man in a bulky gray plugsuit with a full helmet obscuring his face.

"NERV vessel, please identify yourself. You are in a restricted battle zone."

Great, she couldn't even trust herself not to sound official after brushing so close to death. These newfound personality traits baffled her. Those drugs must have been very strong to suppress her persona.

"Don't worry First Child. I'm on your side."

* * *

 **End Note:** Slightly shorter chapter and I feel like its rushed but what the heck. On a side note, know that I'm just making this up as I go along so I decided to cut it here. I forgot to mention that this is writing exercise and I intend to finish it. Forgive me if I update later as the story progresses because I have to keep everything coherent till the end. Thanks again for reading.


	3. Chapter 3

**Author Note:** As usual here's an update. This'll be the third chapter giving a background of both the First Child and Vice Commander. Some of you may wonder why I do dialog this way also (considering a part of this chapter has a lengthy exchange). This is due to Ernest Hemingway and his style of writing character dialog. It feels more natural for me because it's how a conversation would really go in real life (that's just my opinion though). Anyway, enjoy the chapter and I hope it doesn't feel too rushed. (the last part was a bit rushed honestly.)

 **Disclaimer:** I do not own Evangelion or anything related to it. I only write stuff.

* * *

 **09-24-2007 / Gehirn Medical Ward India**

"Today is the 24th of September 2007. Time is 8:00 pm. Session number 7 of 10."

The doctor put down the tape recorder while keeping it on constant record. In front of him was a very remarkable feat only achieved through advancements in bio science. Clearing his throat, the doctor addressed the being in front of him.

"What is your name?"

"Ayanami, Rei."

"What is your purpose?"

"To follow the NERV Commander's orders and to become a pilot for the EVA program."

"Good, good. How old are you?"

"2 days old."

"Physically speaking if you please."

"I possess the visage of a 6-year old sir."

The answers were delivered clinically with an almost detached tone. The subject, one Rei Ayanami, was currently staring at the far wall, the Doctor's presence seemingly forgotten. It had taken merely a day for their drugs to settle in. The product? A being capable of following any order given to them even if it were to the detriment of their being. She was essentially a puppet. Just what the Commander ordered.

"Subject is responsive to suppressant treatments. Advise further observation but otherwise I am declaring the subject fit for active duty."

At his proclamation, two black suited men entered the room. One flanked his seat and another began stopping the recording. Pocketing the device, the second man tugged at the subject's arm and escorted her from the room. Before the doctor could ask what was happening, he heard the door slam shut behind him. The doctor was alone with the last black suited man in the room. A new tape recorder was placed in front of him. The man gestured to the doctor to play the tape. Swallowing audibly, the now nervous doctor pressed play. Immediately, a voice sprung from the small device.

"Good evening Dr. Hashimoto. Congratulations on the developments made on the First Child. I would commend your department on their work if not for the fact that you no longer officially exist."

The tape cut and the doctor turned to face what would appear to be the Section 2 agent in the room. Petrified in fear, the doctor could not form words. He was distraught and shaking life a leaf. Meanwhile, the agent's face betrayed no emotion. The black sunglasses reflected the doctor's face back at him and all he saw was the face of absolute terror staring back. Trying to escape, the doctor lunged at the door handle. Two muffled reports could be heard as the agent unloaded two bullets into the doctor's cranium.

Minutes after the doctor's demise, the Gehirn Medical Ward based in India was lit aflame. The once proud establishment that stood as testament to man's continuous advancements in the medical field burned as quickly as any common building. The fire inched upward and painted the evening a bright orange. The smoke carried the cries of all the men and women who worked there far into the night sky; remnants if nothing else.

* * *

 **12-20-2009 / Gehirn Institute in Tokyo-3, observation deck of the First Child's Training Room**

"She looks like Yui."

"I am aware of that Vice Commander."

"How could you treat someone akin to flesh and blood like this?"

"She is merely a key factor in my plans for the Human Instrumentality Project."

"She is a human being, Gendo."

"She is a clone, Kozo. Nothing more."

"Is that all you see? A means to an end?"

"Enough."

"I cannot let this rest. This is not right."

"Need I remind you that I am the Commander of NERV?"

"I am aware, Commander. But I stand by my decision to wean her off of the suppressants if nothing else."

"On what grounds?"

"I see her as a daughter I could have had, had this world not gone to hell as it is. I saw that in Yui and I see a chance with Rei."

"Your ideal would be realized during Instrumentality. Surely you know this?"

"Consider is a dying man's last wish."

"I cannot grant it."

"Let her lead a normal life and I will personally see to it that when the time comes, she is ready to become the key for Instrumentality."

"What do you derive from a scenario such as that?"

"A chance at happiness, old friend, however brief it might be."

"I will think on your suggestion."

"That is all I ask, Commander."

* * *

 **11-25-2010 / Gehirn Institute in Tokyo-3**

"He sees you as an old hag. You are now no longer useful to him upon the completion of the MAGI."

Naoko Akagi saw red. The thing, a bastardization of Yui Ikari, dared to trivialize her. She knew Gendo would never take her affections seriously. She knew that what they had was purely physical. But to see the face of her rival tell her that Gendo considered her as something to throw away as easily as yesterday's trash was revolting. It made her blood boil staring at the stoic face; a copy of Yui. Something Gendo could never get rid of. Before she knew it she was on her knees with her hands firmly gripping the First Child's neck. She wanted to kill. She wanted to end this last memory of the Commander's wife on Earth. The First Child's eyes bulged as her circulation was cut off. In a few more seconds she would be dead and Naoko Akagi would be rid of the pest. The First Child tried grasping at her arms but she was still too weak from the testing done to her earlier that day. It was futile. Naoko let out a maniacal laugh as she watched the light begin to expire from the thing's eyes. She was, however, destined to be denied her revenge. For at that time, one Kozo Fuyutsuki was sent to inquire about the status of the MAGI. His presence was soon announced by the click of a gun's safety being removed.

"Unhand the First Child, Doctor. You have 3 seconds to comply."

Staring at the Vice Commander in bewilderment, Naoko could only wonder why he was defending the abomination. 3 seconds passed without the Doctor relinquishing her grip and a single shot echoed throughout the massive super computer chamber. A single bullet case fell and a single body slumped to the floor. In an instant, it was over. Blood poured from the Doctor's abdomen as the 9mm punched through her flimsy lab coat like a knife on butter. The Vice Commander casually walked towards the gasping First Child. He picked her up and set her a few feet away from the doctor. Turning back, he addressed Naoko.

"Is the MAGI completed?"

"Get me a medical team, you crazy old man!"

"Is the MAGI completed?"

"I'm fucking bleeding out!"

"Is the MAGI completed, Dr. Akagi?"

"It is you miserable coot! The greatest invention known to man is completed and here you are killing the inventor!"

"Goodbye Naoko."

Another gunshot rang out and Dr. Naoko Akagi dropped onto the floor. Dead due to massive head trauma; the work of lead punching through brain matter. The Vice Commander then holstered his weapon and gingerly picked up the First Child; carefully assessing her condition. Without breaking stride, he reached the lifts and signaled one to come. Facing one of the multiple surveillance cameras in the room, Kozo Fuyutsuki addressed his Commander.

"I take full responsibility. Trust in me this once."

A week later, no official inquiry was made about the death of Naoko Akagi. All the reports that came from half-assed investigations pointed towards the same conclusion, that the stress had led her to suicide. Kozo knew what had happened and he was glad that Gendo had pulled strings to spare him. It would seem that the Commander had indeed no further use for the former Gehirn scientist.

* * *

 **09-22-2011 / Tokyo-3, the residence of Kozo Fuyutsuki**

"Rei, it's time to get up. You'll be late for school."

The somewhat groggy bluenette rose up and rubbed at her eyes.

"I am sorry Vice Commander, withdrawal from the drugs seems to have an effect on my sleep cycle. I will endeavor to rectify this in the future."

Shaking his head in amusement, the Vice Commander of NERV watched as his young charge struggled to stand up. Rei had grown considerably well ever since Kozo had managed to liberate her from the NERV HQ. Gendo had acquiesced to his petition to transfer Rei into his domicile and the Vice Commander could not be happier for it. He knew that this only meant that Gendo had agreed to the deal he had off handedly made years prior. Right now, however, he could care less. His charge exited her room dressed in her middle school uniform. A sight Kozo would commit to memory as something he would always remember Rei by; the visage of innocence.

"Have you taken a bath?"

"I showered last night, Vice Commander."

"Do you want breakfast?"

"A child of my age should not be denied the proper sustenance needed to function. I would like some eggs."

"I'll see what I can do."

With that, the Vice Commander and the First Child formed the most unlikely of relationships: one of father and daughter; a beacon of good in their dark times.

* * *

 **07-14-2013 / NERV HQ Tokyo-3**

The First Child, now 12 years of age, was currently inside the EVA simulation room. A dummy synch would be set up to mimic the feeling of a neural handshake between an EVA and a human. The test was that of a combat simulation. It had been a year since the Science Department had declared her fit for active training. This meant that she had less time for school and more time for testing within NERV. The new Head of Science was none other than Naoko Akagi's daughter, Ritsuko. Dr. Akagi was indifferent towards Rei. It was either she knew and did not care about her mother's death, or that she was secretly planning to kill Rei. The First Child did not know the answer and she did not care to find out. Presently, both were civil with one another and that was enough for both.

"Rei, you need to keep your head clear. It'll be easier to synch during the activation test that way. Right now we have erratic readings all around. Have you been taking your meds?"

"I have, Dr. Akagi."

"That's odd. I do hope the Vice Commander keeps you up to speed with your medicine."

"The Vice Commander oversees my daily medical intake Dr. Akagi. It is of no concern."

"If you say so, Rei. Go ahead and change into your plugsuit. We need more information on your combat abilities."

"Acknowledged Doctor. I will proceed to the pilot changing rooms."

Turning about and walking towards the said rooms, the First Child breathed a sigh of relief. It was getting harder to control her emotions as of late. It was a chore to pretend to be emotionless in front of the Doctor, but the Vice Commander had advised her against revealing her newfound persona. The reason being that the Commander had only unofficially approved of her stopping her suppressants. On paper, and to everyone else's knowledge, Rei Ayanami was still a heavily sedated EVA pilot of NERV. Only the Vice Commander and the Commander knew of her real self. Shaking to clear her head, the First Child began to don her plugsuit and A-10 clips. After making sure that her face did not betray her frustration at the exercise, Rei exited the changing room and proceeded towards the simulation plug. A series of overhead light illuminated the suspended mock entry plug while a series of wires connected it to various outlets of the MAGI. Clambering on board, the plug powered up and a simulation synch was achieved using the seat interface and the plugsuit material. Rei felt aware of a second presence in her mind as she began running through the basic routine of EVA piloting.

"How's the dummy synch Rei? Anything feel out of place?"

"It is still the same as the last synch Dr. Akagi. I suggest we proceed to the simulation so gather further information."

"Okay Rei, brace yourself."

The main screen flickered to life and Rei was assaulted by the scene of a beautiful mountainside. The only thing out of place was the vaguely humanoid shape that was lumbering towards her. Going through the basics of piloting, Rei brought up her Friend-or-Foe indicator and began assessing the target. 'EVA Unit-00' it said as the report came back. Puzzled, she keyed in her communications code for Dr. Akagi.

"Dr. Akagi, it would seem that the simulation is broken. The simulation EVA FoF indicator suggests that I am against my own EVA."

"No anomalies Rei. Today's exercise has you against Unit-00 with a different pilot in it."

"A simulation pilot, Doctor?"

"No. More of like data from an existing pilot."

"May I ask who?"

"Classified information Rei. Can't have myself spilling all of NERV's dirty secrets."

"Acknowledged, Doctor. I will try my best to combat the threat."

Taking a shaky breath, the First Child readied herself to face her opponent. It looked like there were actually other pilots besides her. She silently laughed at the notion that she had thought she was the only one. Focusing back on the mission, Rei began moving her EVA at a steady pace to approach the target. The instructors told her that she should first focus on walking before moving on to more advanced movements. Her opponent, it seemed, had not listened to her batch of instructors. The enemy Unit-00 moved with an unnatural grace. Sprinting towards her and then stopping to circle her EVA. The enemy Unit-00 had drawn its Progressive Knife and had started to brandish it menacingly as if baiting her to attack. After managing to assume the proper stance for fighting, Rei had her EVA draw its own prog-knife. Without warning, the enemy EVA leapt forward. Covering the distance in the blink of an eye. A second later and Rei found her EVA's head flying from the body. External display cut out and the simulation terminated.

"Rei, were you even trying?"

"I could not match his speed Dr. Akagi. The EVA motion trackers could not compensate and I could not eyeball his movements effectively to mount a defense. It seems he or she is a far more advanced pilot than I."

"You're probably right but that doesn't excuse your failure to react. I'll have to talk to your instructor's regarding your training regimen."

"I understand Dr. Akagi. I promise to try doing better in the future."

"Don't burn yourself out kid. My mom used to be all business and look where that got her. You need to lighten up every once in a while."

Rei could only nod in her direction while she tried to hide the nervousness she felt at knowing that Ritusko Akagi did not know how her mother had died. The bluenette bid farewell and strode out of the room as fast she could while still looking calm. She needed to vent to the Vice Commander else she explode in frustration. These emotions were truly troublesome.

* * *

 **05-25-2015 / NERV HQ Tokyo-3**

NERV HQ was positively bustling. Word had gotten around that today would be EVA Unit-00's Activation Test; big news for the facility's recent lack of action. Presently, Dr. Ritsuko Akagi was reviewing the First Child's synchronicity graphs from the dummy synch system. The data indicated that the First Child should achieve at least 20% synch during the actual test. A long shot from the Third Child's test but good enough for a newbie pilot; at least by the MAGI's standards. The First Child had not performed spectacularly in the past months' simulations. Regardless, the Commander had given the go ahead for the Unit's activation. Chief reason above all was that they needed a fully functional and combat ready EVA and pilot tandem in case of an emergency. The Doctor understood the need as well. Even with the existence of the prodigious Third Child, he was currently still on the moon. Too far to react quickly enough. With a sigh, Dr. Akagi clutched her data clipboard and proceeded to check up on the pilot. Said pilot was currently inside the pilot changing rooms, brooding by the looks of it. Deciding to interrupt her thought, the Doctor sat beside Rei.

"Are you nervous?"

"I do not know what to feel Dr. Akagi."

"Well in any case, it's okay to be nervous. I know I am and I'm not even the test subject."

The jab coaxed the First Child into looking slightly more determined. Taking that as a sign to continue, the doctor began reassuring Rei.

"Your latest synchronicity graph showed a 5.4% increase. That should translate well into the actual test."

"Thank you Dr. Akagi. I shall try to make you proud."

The phrase earned Rei a questioning look from the Doctor.

"The Vice Commander informed me that saying the phrase is the appropriate response to encouragement. I assumed that you had been trying to reassure me Doctor. Was I wrong in my assumption?"

Dr. Akagi bit back a laugh at the bluntness of the First Child. In a way it reminded her of the early days where she had nothing to worry about. It was refreshing.

"You were correct with your assumption. Although most times you needn't explain your choice of words to your audience."

With a snicker, the Doctor motioned for Rei to stand up and both proceeded out of the locker room, spirits lifted if only slightly. Dr. Akagi watched as the First Child exited through the right most blast door and proceed to the entry plug loading area. Overhead, a series of speakers began dishing out orders.

"Attention on the deck! Evangelion Unit-00 Activation Test will commence in 5 minutes. All non-essential personnel, please clear the action deck for testing."

People started exiting the launch bay as the remaining crew battled to get the EVA ready. Dr. Akagi strode towards the NERV HQ Command Room and was greeted by the sight of both the Commander and Vice Commander.

"I hope this evening finds you well Dr. Akagi."

"I would say the same for you Vice Commander."

The Vice Commander merely gave a non-committal shrug and proceeded to inch closer towards the view deck, essentially abandoning his post beside the Commander. Filing away the curious behavior for later, the Doctor gripped the intercom mike and announced the final stages of preparation over the action deck.

"Launch crew please vacate the EVA cage. Command Room crew prepare for entry plug insertion."

"Copy that Doctor. Removing primary and secondary EVA cage locks. Primary umbilical is ready. Spinal connection established, proceeding to eject the transmission plug."

"Plug is away. Inserting Unit-00 entry plug. Standby."

The whine of various machinery echoed throughout the action deck as the entry plug was inserted into the EVA.

"Entry plug is secured. Flooding plug in 3, 2, 1."

Inside the plug, Rei held her breathe until the last moment before breathing in the LCL. It felt alien to be breathing in that manner but she had experienced worse. Swallowing her discomfort, the First Child began cycling through her system checks and audibly checking in for launch just like she was trained to do.

"Pilot to bridge, EVA system is at 100% functionality. First Child is ready for neural handshake."

"Copy that First Child. Initiating neural handshake and beginning EVA synch."

A kaleidoscope of images assaulted her mind. A myriad of colors flashed by and Rei felt herself floating. A wave of nausea racked her frame but soon passed. The First Child felt as if something was in her mind and it was not friendly in any way. A second presence surfaced and sifted through her now jumbled thoughts. It was nerve-wracking to be subjected to such an investigation.

"First Child neural handshake accepted, ma'am. Synch ratio is holding at 24%. Barely enough but it's holding."

"Activation achieved! Congratulations First Child!"

Applause could be heard throughout the facility as the various tech crews congratulated one another on a job well done. The celebrations were short lived, unfortunately.

"Ma'am! We have a spike in mental activity!"

Inside, Rei felt a different emotion surface. She felt the need to smash something. It was an encompassing notion. More of an order than a suggestion.

 _KILL! HE DOES NOT CARE FOR US! HIS FAULT!_

The thoughts formed faster than Rei could process them. Without warning, the EVA began stumbling towards the Command Room's view deck.

"Ma'am, signs of mental contamination have been detected! The pilot is unresponsive!"

"Detach the primary umbilical and eject the entry plug."

"Detaching! EVA is unresponsive to ejection."

The EVA continued to lumber forward. With a shocking display of awareness, the EVA turned its eye toward the view deck and glowed an unnatural red. With a flourish, the EVA raised one of its fists and began pounding away at the tempered view glass. The Command Room was rocking in motion as Unit-00 hammered away with its fists. Hairline cracks were beginning to form on the view deck glass. The technicians were backing away in fear. Only the Commander and Vice Commander remained in place. The former observing and the latter trying to communicate with the pilot.

"Rei! You have to fight it!"

"It is of no use Vice Commander. Action deck crew, deploy countermeasures."

Kozo Fuyutsuki could only look onward in horror as bakelite streamed into the room. The fast setting resin poured onto the EVA and began immobilizing parts of it. As the stream of bakelite winded down, the Evangelion fired off its final parting shot in the form of an ejecting entry plug. The Vice Commander could only watch as the plug flew at an arc and collided with the EVA cage. The resulting trip down was even worse as the plug caught unto the metal girders during free fall. Despite the danger, Kozo ran full tilt to lift. Uncharacteristic for a man his age. The lift took him directly down to the action deck where he rushed to the fallen entry plug. He grasped at the manual release for the magnetic doors and cried out in pain as the metal radiated with heat. Hands now burned, the old professor pulled and managed to open the door. Rei was floating in the warm LCL, clearly unconscious. The Vice Commander carried her out and proceeded to assess her condition. Medical teams began flanking him but he only had eyes for his surrogate daughter. While the First Child was wheeled away in a gurney, the Commander was smirking to himself at the view. The scientists he had assigned to quickly salvage Naoko's soul had done a marvelous job. Replacing it without anyone's knowledge into Unit-00 had been child's play. And judging by the EVA's actions, it would seem that Naoko still hated him. The implications of this hate was tremendous. All the First Child needed to do now was synch properly and all further berserker tendencies would be nullified. It could be channeled on the battlefield instead of towards him. It put his plans back on track ever since NERV Luna had reported that the Third Child had almost full control of Unit-01; testament to his training and talent. That closed the door towards harnessing Yui's paternal instinct to protect Shinji, leaving the Commander without a wildcard. This new development should, however, suffice. Motioning one of the Section 2 agents to approach him, Gendo gave the final orders for today's experiment.

"Please send my congratulations to one Dr. Morimoto and his team. Tell them, exceptional job on replacing the soul."

"Terminate with discretion, Commander?"

"Yes agent. Discretion is key."

* * *

 **End Note:** Most of the history is probably butchered by now so I stress it again. AU my friends. Till next time. Also forgive me if I have spelling or grammar issues. I mostly just go over the work twice and if I don't spot the wordier or the weirdly written parts then it stays and I apologize. - for some reason ff dot net says 'apologize' is spelled wrong. Go figure.


End file.
